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UCLA
In division 1 it's probabilly the university of Washington.
UCLA holds the record for the most NCAA Men's Division
Alabama, with 33 bowl victories out of 58 appearences and 14 national championships.
Larry Kehres, of Mount Union College, Division III, with 9 national championships.
The UCLA Lady Bruins have won the most National Championships in Collegiate Fastpitch Softball...I believe they have won 25 or 26 National Championships.
Stanford with 6 NCAA Titles (1992, 1994, 1996, 1997, 2001, 2004)
UCLA has won 11 NCAA mens championships. Tennessee has won 8 NCAA women's championships.
For the category of Division I sports in the men's and women's field, the university that has the most NCAA championships is UCLA. They have 109 as of 2012. Stanford is next with 103, followed by USC with 96.
Minnesota Duluth Bulldogs have won 4; 2001, 2002, 2003, 2008.
UCLA with 11 championships.